Update for new nim

frameshiftgenomics · Feb 11, 2019 · 6e79bb8 · 6e79bb8
1 parent a362541
commit 6e79bb8
Show file tree

Hide file tree

Showing 2 changed files with 9 additions and 3 deletions.
diff --git a/README.md b/README.md
@@ -1,3 +1,9 @@
+Frameshift note: build with the latest nim (as of this writing, v0.19.4).
+To build: 
+1) `nimble install -y`
+2) `nim c -d:release mosdepth.nim`
+
+
 fast BAM/CRAM depth calculation for **WGS**, **exome**, or **targeted sequencing**.
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/recipes/mosdepth/README.html)
 

diff --git a/stats.nim b/stats.nim
@@ -23,7 +23,7 @@ type
     fragLengthHist: CountTableRef[int]
     readLengthHist: CountTableRef[int]
 
-proc countRead*(rs: var bamStats, rec: Record, chrom: string = nil) = 
+proc countRead*(rs: var bamStats, rec: Record, chrom: string = "") = 
   rs.totalReads += 1
   if rec.flag.proper_pair:
     rs.properPairs += 1
@@ -45,7 +45,7 @@ proc countRead*(rs: var bamStats, rec: Record, chrom: string = nil) =
       if rec.flag.mate_unmapped: rs.singletons += 1
       else: rs.bothMatesMapped += 1
 
-  if chrom != nil:
+  if chrom != "":
     rs.refAlnHist.inc(chrom)
     #if not rs.refAlnHist.hasKey(chrom):
     #  rs.refAlnHist[chrom] = 0
@@ -130,4 +130,4 @@ proc to_json*(rs: bamStats): string =
     js["length_hist"].add($length, newJInt(count))
 
   return js.pretty()
-
+